Parameters

The parameters described below can be specified when the pipeline is run. They change the behavior of various stages.

Output

output_dir

A local directory in which to write the final output files, including the aggregated results and error reports. A reasonable choice would be '${launchDir}/output'.

Protein Receptor (Pocket)

The values below describe the protein receptor we will “grow” molecules for in the denovo step.

receptor_pdb

Description of the protein receptor, in PDB format.

receptor_center_x

X coordinate of the pocket center

receptor_center_y

Y coordinate of the pocket center

receptor_center_z

Z coordinate of the pocket center

receptor_size_x

size in the X dimension (Angstroms)

receptor_size_y

size in the Y dimension (Angstroms)

receptor_size_z

size in the Z dimension (Angstroms)

Denovo (Stage 3)

seed_ligands (optional)

A SMILES file (.smi) containing one or more SMILES strings for molecules to use in place of building denovo ligands with Autogrow4. This causes Stage 3 to be skipped, the ligands specified will be fed directly into Stage 4.

autogrow_exhaustiveness

The value to use for the docking_exhaustiveness parameter to Autogrow4. The default is 1.

autogrow_generations

The number of generations to produce with Autogrow4. Drug Sniffer uses the last three generations, so this value must be at least 3. The default is 20.

Similarity Search (Stage 4)

molecule_db

The path to the molecule database to use.

tanimoto_cutoff

The minimum Tanimoto coefficient to consider two molecules a match.

ADMET Prediction (Stage 7)

admet_checks

A space-separated list of ADMET checks to perform, see the FPADMET documentation for a list of available checks.